Fig. 1.

Performance evaluation of the new nontryptic MS²PIP models. Boxplots comparing Pearson correlation distributions between predicted and observed peak intensity values on spectrum level for the 2019 HCD model, immunopeptide model, nontryptic immunopeptide model, and immuno-chymotrypsin model. Performance is evaluated on general tryptic proteomics data, HLA-I immunopeptide data, HLA-II immunopeptide data, and chymotrypsin data (A). Predictions for immunopeptide “KQHGVNVSV” by new immunopeptide MS²PIP model (top) compared to observed MS2 spectrum (mzspec:PXD005231:20160513_TIL1_R1:scan:10909) (bottom) (B). This peptide was selected for visualization as its PCC lies close to the median for the immunopeptide model on all HLA-I evaluation data. Predictions by the 2019 HCD model for the same immunopeptide (C) as visualized in B. HCD, higher-energy collision-induced dissociation; MS2, tandem mass spectrometry; PCC, Pearson correlation coefficient.